scholarly journals Time and Space in Segmentation

2020 ◽  
Author(s):  
Erik Clark
Keyword(s):  
Spatial Information ◽  
Positional Information ◽  
Coarse Grained ◽  
Spatial Organisation ◽  
Scaling Relationships ◽  
Evolutionary Origins ◽  
Developmental Patterning ◽  
Wave Patterns ◽  
Axial Variation ◽  
Oscillator Output

AbstractArthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include (1) the mechanistic origins of spatial organisation within the segment addition zone (SAZ); (2) the mechanistic origins of segment polarisation; (3) the mechanistic origins of axial variation; and (4) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an “oscillator”, a “switch”, and up to three “timers”, successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns, and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarising oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.

scholarly journals Time and space in segmentation

2021 ◽  
Vol 11 (3) ◽  
Author(s):  
Erik Clark
Keyword(s):  
Spatial Organization ◽  
Spatial Information ◽  
Positional Information ◽  
Coarse Grained ◽  
Scaling Relationships ◽  
Evolutionary Origins ◽  
Developmental Patterning ◽  
Wave Patterns ◽  
Axial Variation ◽  
Oscillator Output

Arthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include: (i) the mechanistic origins of spatial organization within the segment addition zone (SAZ); (ii) the mechanistic origins of segment polarization; (iii) the mechanistic origins of axial variation; and (iv) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an ‘oscillator’, a ‘switch’ and up to three ‘timers’, successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarizing oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.

Volumes and Surface Areas: Geometries and Scaling Relationships between Coarse- Grained and Atomic Structures

2014 ◽  
Vol 20 (8) ◽  
pp. 1208-1222 ◽  
Author(s):  
Daniel Flatow ◽  
Sumudu Leelananda ◽  
Aris Skliros ◽  
Andrzej Kloczkowski ◽  
Robert Jernigan
Keyword(s):  
Coarse Grained ◽  
Atomic Structures ◽  
Scaling Relationships ◽  
Surface Areas

Development of a Communication Aid App with iOS Devices to Support Children/Persons with Speech Disabilities Improvement in Obtaining Positioning Information with iBeacon as Near Field Radio Communication Technology

2017 ◽  
Vol 21 (2) ◽  
pp. 371-377
Author(s):  
Tomonori Karita ◽  
Keyword(s):  
Correct Answer ◽  
Social Life ◽  
Spatial Information ◽  
Near Field ◽  
Positional Information ◽  
Radio Communication ◽  
Communication Aid ◽  
Research Task ◽  
Speech Disabilities ◽  
Gps System

Communication has such a vital function as the foundation of human social life that speech disabilities can drastically deteriorate people’s quality of life. The author has developed a voice output communication aid (VOCA) to enable children/persons with speech disabilities to communicate with other people according to conversation situations with iOS devices with global positioning system (GPS), positional information acquiring technology (iBeacon), and a clock function installed. The developed technology is an application compatible with iOS (hereinafter, app) that displays a list of messages (hereinafter, VOCA interface) if any of them correspond to the information on the user’s location and time of use as acquired by users with a portable information device with a GPS function, iBeacon function, and clock function installed. Users can communicate by selecting the icons of required messages from VOCA interfaces to reproduce registered voice data instead of their own voices. We have named the developed technology “Friendly VOCA” because its intentions are that: (1) users can communicate with other people with as few operations involved as possible; (2) it should be easy for users to learn and to operate. This paper reports the development processes of the Friendly VOCA and defines the ratios of preregistered VOCA interfaces displayed (hereinafter, correct answer rates) in acquiring positional information with GPS and with iBeacon. In Research Task 1, we have conducted experiments to verify the correct answer rates of the GPS system in outdoor use of the Friendly VOCA and in Research Task 2 we have conducted experiments to verify the correct answer rates of the iBeacon system in indoor use of the Friendly VOCA. The research results show that both the GPS system and iBeacon system can specify user’s spatial information and display appropriate lists of messages. However, the experiments found that iBeacon signal transmitters can transmit signals over a distance of 50 m or more: to improve the correct answer rates of the iBeacon system, we may need to increase the distance between iBeacon signal transmitters or select devices with a shorter range of transmission.

scholarly journals Gradients of Rac1 nanoclusters support spatial patterns of Rac1 signaling

2017 ◽  
Author(s):  
Amanda Remorino ◽  
Simon De Beco ◽  
Fanny Cayrac ◽  
Fahima Di Federico ◽  
Gaetan Cornilleau ◽  
...  
Keyword(s):  
Single Molecule ◽  
Spatial Information ◽  
Local Density ◽  
Local Level ◽  
Super Resolution ◽  
Positional Information ◽  
Supramolecular Organization ◽  
Local Concentration ◽  
Intracellular Space ◽  
Rac1 Activity

AbstractThe dynamics of the cytoskeleton and cell shape relies on the coordinated activation of RhoGTPase molecular switches. Among them, Rac1 participates to the orchestration in space and time of actin branching and protrusion/retraction cycles of the lamellipodia at the cell front during mesenchymal migration. Biosensor imaging has revealed a graded concentration of active GTP-loaded Rac1 in protruding regions of the cell. Here, using single molecule imaging and super-resolution microscopy, we reveal an additional supramolecular organization of Rac1. We find that, similarly to H-Ras, Rac1 partitions and is immobilized into nanoclusters of 50-100 molecules each. These nanoclusters assemble due to the interaction of the polybasic tail of Rac1 with the phosphoinositide lipids PIP2 and PIP3. The additional interactions with GEFs, GAPs, downstream effectors, and possibly other partners are responsible for an enrichment of Rac1 nanoclusters in protruding regions of the cell. Using optogenetics and micropatterning tools, we find that activation of Rac1 leads to its immobilization in nanoclusters and that the local level of Rac1 activity matches the local density of nanoclusters. Altogether, our results show that subcellular patterns of Rac1 activity are supported by gradients of signaling nanodomains of heterogeneous molecular composition, which presumably act as discrete signaling platforms. This finding implies that graded distributions of nanoclusters might encode spatial information.Significance statementThe plasma membrane of eukaryotic cells is a highly organized surface where hundreds of incoming signals are transduced to the intracellular space. How cells encode faithfully this myriad of signals is a fundamental question. Here we show that Rac1, a critical membrane-bound protein involved in the regulation of cytoskeletal dynamics, forms small aggregates together with other regulating proteins. These supramolecular assemblies, called nanoclusters, are the “quantal” units of signaling. By increasing the local concentration, nanoclusters set thresholds for downstream signaling and ensure the fidelity of information transduction. We found that Rac1 nanoclusters are distributed as spatial gradients matching the patterns of Rac1 activity. We propose that cells can encode positional information through distributed signaling quanta, hereby ensuring spatial fidelity.

scholarly journals Stable encoding of visual cues in the mouse retrosplenial cortex

2019 ◽  
Author(s):  
Anna Powell ◽  
William M. Connelly ◽  
Asta Vasalauskaite ◽  
Andrew Nelson ◽  
Seralynne D. Vann ◽  
...  
Keyword(s):  
Visual Cues ◽  
Spatial Information ◽  
Sensory Information ◽  
Positional Information ◽  
Retrosplenial Cortex ◽  
Single Neurons ◽  
Sensory Data ◽  
Longitudinal Measurements ◽  
Directional Preference ◽  
Evoked Activity

Abstract The rodent retrosplenial cortex functions as an integrative hub for sensory and motor signals, serving roles in both navigation and memory. While retrosplenial cortex (RSC) is reciprocally connected with the sensory cortex, the form in which sensory information is represented in the retrosplenial cortex and how it interacts with behavioural state is unclear. Here, we used 2-photon cellular imaging of neural activity of putative excitatory (CaMKII expressing) and inhibitory (parvalbumin expressing) neurons to measure visual and running evoked activity in RSC and compare it to primary visual cortex (V1). We found that stimulus position and orientation information was preserved between V1 and RSC, and additionally that positional information was organised topographically. Stimulus directional preference was biased towards nasal-temporal flow. Locomotion modulation of activity of single neurons, both in darkness and light, was also more pronounced in RSC than V1, and strongest in parvalbumin-positive neurons. Longitudinal measurements of single neurons showed that these response features were stably maintained over many weeks. These data provide evidence for stable representations of visual cues in retrosplenial cortex which are highly spatially selective. These may provide sensory data to contribute to the formation of memories of spatial information.

The Effect of Visuo-Spatial Organisation in Recognition-Memory Tasks

Perception ◽  
10.1068/p6095 ◽  
2009 ◽  
Vol 38 (5) ◽  
pp. 763-774
Author(s):  
Laura Petrini ◽  
Kristian Hennings ◽  
Lars Arendt-Nielsen
Keyword(s):  
Recognition Memory ◽  
Spatial Information ◽  
Visual Stimuli ◽  
Spatial Task ◽  
Verbal Task ◽  
Verbal Information ◽  
Spatial Organisation ◽  
Male Volunteers ◽  
Stimulus Probe ◽  
Left And Right

We investigated whether recognition memory benefits when stimuli are organised in a visuo-spatial array. Three different memory tasks were compared: (a) verbal task (what); (b) spatial task (where); (c) combination task, where both verbal and spatial informations were combined together (what/where). We hypothesised that when visual stimuli are organised in a spatial array the recognition is better. Recognition memory was assessed by quantifying the speed of correct responses and the total number of correct responses in a group of male volunteers ( N = 20). Subjects' task was to recognise a stimulus probe from sequences (one versus three) of stimuli. All stimuli appeared randomly in one of nine locations on a 3 × 3 grid. The results show that subjects were faster and more accurate when they had to recognise only spatial information (where) than when they had to recognise verbal information (what) or the combination of both verbal and spatial information (what/where). Additionally, when the stimuli were presented in a spatial array there were benefits for the spatial task, whilst verbal and combination tasks were unaffected. Additionally, asymmetry between left and right hemifields has been found. These findings are discussed with regard to different memory processes that operate independently.

scholarly journals The FGLOCTweet Corpus: An English tweet-based corpus for fine-grained location-detection tasks

2022 ◽  
Vol 10 (1) ◽  
pp. 117-133
Author(s):  
Nicolás José Fernández-Martínez
Keyword(s):  
Social Media ◽  
Language Processing ◽  
Situation Awareness ◽  
Spatial Information ◽  
Emergency Situation ◽  
Coarse Grained ◽  
Text Data ◽  
Emergency Responders ◽  
Fine Grained ◽  
Location Detection

Location detection in social-media microtexts is an important natural language processing task for emergency-based contexts where locative references are identified in text data. Spatial information obtained from texts is essential to understand where an incident happened, where people are in need of help and/or which areas have been affected. This information contributes to raising emergency situation awareness, which is then passed on to emergency responders and competent authorities to act as quickly as possible. Annotated text data are necessary for building and evaluating location-detection systems. The problem is that available corpora of tweets for location-detection tasks are either lacking or, at best, annotated with coarse-grained location types (e.g. cities, towns, countries, some buildings, etc.). To bridge this gap, we present our semi-automatically annotated corpus, the Fine-Grained LOCation Tweet Corpus (FGLOCTweet Corpus), an English tweet-based corpus for fine-grained location-detection tasks, including fine-grained locative references (i.e. geopolitical entities, natural landforms, points of interest and traffic ways) together with their surrounding locative markers (i.e. direction, distance, movement or time). It includes annotated tweet data for training and evaluation purposes, which can be used to advance research in location detection, as well as in the study of the linguistic representation of place or of the microtext genre of social media.

scholarly journals Steady-state invariant genetics: probing the role of morphogen gradient dynamics in developmental patterning

2011 ◽  
Vol 8 (63) ◽  
pp. 1429-1439 ◽  
Author(s):  
Marcos Nahmad
Keyword(s):  
Steady State ◽  
Dynamic Properties ◽  
Positional Information ◽  
Design Tool ◽  
Maximum Width ◽  
Animal Development ◽  
Gradient Dynamics ◽  
Developmental Patterning

Morphogen-mediated patterning is the predominant mechanism by which positional information is established during animal development. In the classical view, the interpretation of positional signals depends on the equilibrium distribution of a morphogen, regardless of the dynamics of gradient formation. The problem of whether or not morphogen dynamics contribute to developmental patterning has not been explored in detail, partly because genetic experiments, which selectively affect signalling dynamics while maintaining unchanged the steady-state morphogen profile, are difficult to design and interpret. Here, I present a modelling-based approach to identify genetic mutations in developmental patterning that may affect the transient, but leave invariant the steady-state signalling gradient. As a case study, this approach is used to explore the dynamic properties of Hedgehog (Hh) signalling in the developing wing of the fruitfly, Drosophila melanogaster . This analysis provides insights into how different properties of the Hh gradient dynamics, such as the duration of exposure to the signal or the maximum width of the transient gradient, can be genetically perturbed without affecting the steady-state distribution of the Hh concentration profile. I propose that this method can be used as an experimental design tool to investigate the role of transient morphogen gradients in developmental patterning and discuss the generality of these ideas in other problems.

scholarly journals Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data

2021 ◽  
Vol 11 ◽  
Author(s):  
Phillipe Loher ◽  
Nestoras Karathanasis
Keyword(s):  
Machine Learning ◽  
Single Cell ◽  
High Performance ◽  
Spatial Information ◽  
Model Organism ◽  
Positional Information ◽  
Learning Approaches ◽  
Sequencing Data ◽  
Weak Supervision ◽  
Single Cell Sequencing

The development of single-cell sequencing technologies has allowed researchers to gain important new knowledge about the expression profile of genes in thousands of individual cells of a model organism or tissue. A common disadvantage of this technology is the loss of the three-dimensional (3-D) structure of the cells. Consequently, the Dialogue on Reverse Engineering Assessment and Methods (DREAM) organized the Single-Cell Transcriptomics Challenge, in which we participated, with the aim to address the following two problems: (a) to identify the top 60, 40, and 20 genes of the Drosophila melanogaster embryo that contain the most spatial information and (b) to reconstruct the 3-D arrangement of the embryo using information from those genes. We developed two independent techniques, leveraging machine learning models from least absolute shrinkage and selection operator (Lasso) and deep neural networks (NNs), which are applied to high-dimensional single-cell sequencing data in order to accurately identify genes that contain spatial information. Our first technique, Lasso.TopX, utilizes the Lasso and ranking statistics and allows a user to define a specific number of features they are interested in. The NN approach utilizes weak supervision for linear regression to accommodate for uncertain or probabilistic training labels. We show, individually for both techniques, that we are able to identify important, stable, and a user-defined number of genes containing the most spatial information. The results from both techniques achieve high performance when reconstructing spatial information in D. melanogaster and also generalize to zebrafish (Danio rerio). Furthermore, we identified novel D. melanogaster genes that carry important positional information and were not previously suspected. We also show how the indirect use of the full datasets’ information can lead to data leakage and generate bias in overestimating the model’s performance. Lastly, we discuss the applicability of our approaches to other feature selection problems outside the realm of single-cell sequencing and the importance of being able to handle probabilistic training labels. Our source code and detailed documentation are available at https://github.com/TJU-CMC-Org/SingleCell-DREAM/.

scholarly journals The dynamic transmission of positional information in stau- mutants during Drosophila embryogenesis

2019 ◽  
Author(s):  
Zhe Yang ◽  
Hongcun Zhu ◽  
KaKit Kong ◽  
Jiayi Chen ◽  
Xiaxuan Wu ◽  
...  
Keyword(s):  
Measurement Errors ◽  
Positional Information ◽  
Underlying Mechanism ◽  
Dynamic Changes ◽  
Large Shift ◽  
Large Variability ◽  
Self Organized ◽  
Developmental Patterning ◽  
And Shifts ◽  
Embryo Length

AbstractIntriguingly, the developmental patterning during Drosophila embryogenesis is highly accurate and robust despite its dynamic changes and constant fluctuations. It has been suggested that Staufen (Stau) is key in controlling the boundary variability of the gap protein Hunchback (Hb). However, its underlying mechanism is still elusive. Here, we have developed methods to quantify the dynamic 3D expression of segmentation genes in Drosophila embryos. With improved control of measurement errors, our results reveal that the posterior boundary of the Hb anterior domain (xHb) of stau- mutants shows comparable variability to that of the wild type (WT) and shifts posteriorly by nearly 12% of the embryo length (EL) to the WT position in the nuclear cycle (nc) 14. This observed large shift might contribute significantly to the apparent large variability of xHb in previous studies. Moreover, for stau- mutants, the upstream Bicoid (Bcd) gradients show equivalent gradient noise to that of the WT in nc12-nc14, and the downstream Even-skipped (Eve) and cephalic furrow (CF) show the same positional errors as the WT. Our results indicate that threshold-dependent activation and self-organized filtering are not mutually exclusive but could both be implemented in early Drosophila embryogenesis.

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